Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
Ghost
@ghost~5772e7e2c2f0db084a206e1b
that tool definitely should be reporting what you see inside the collection
which are the element_identifiers
galaxybot
@galaxybot
[jebediah] the dataset name is cILC2 KO IL-25_IL-1b_IL-23_TGFb_IL-6_029.fcs and that is what appears when the extract tool is used. but in the yml file i set element_identifier as abcd
Ghost
@ghost~5772e7e2c2f0db084a206e1b
but what do you see in the UI ?
galaxybot
@galaxybot
[jebediah] i see the long name
Ghost
@ghost~5772e7e2c2f0db084a206e1b
that'd be the simplest check
so something is wrong with the script
galaxybot
@galaxybot
[jebediah] i can show you the contents of the yml file too if you'd like
Ghost
@ghost~5772e7e2c2f0db084a206e1b
sure
Ghost
@ghost~5772e7e2c2f0db084a206e1b
and what script are you using ?
galaxybot
@galaxybot
[jebediah] fetch_to_library.py
Ghost
@ghost~5772e7e2c2f0db084a206e1b
but ... that doesn't import to the history ?
galaxybot
@galaxybot
[jebediah] I found that it can if you specify type: hdca
[jebediah] in the yml file
Ghost
@ghost~5772e7e2c2f0db084a206e1b
alright
name in that case is the element_identifier
so you can't have both
at least that's what the tests are using
galaxybot
@galaxybot
[jebediah] Oh ok
galaxybot
@galaxybot
[jebediah] also, this is not exactly related, but can anything be done with the UUID listed in the job information for a dataset?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
I'm not sure the UUID is that helpful, but you surely can use the dataset id or the job id to track what's going on
galaxybot
@galaxybot
[jebediah] awesome. thanks for the help
Érica Souza
@souzaems
Can someone help using Interproscan at Galaxy? An error occuring during the process and I don't know how to fix
galaxybot
@galaxybot
[enis] @jmchilton Is it possible for Pulsar to use an existing installation of Conda vs. installing it’s own at startup?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
enis: if conda is already present at that location it shouldn't install a new one
IIRC this code is shared between Gaaxy and pulsar
John Chilton
@jmchilton
Should be able to set conda_prefix in your Pulsar config or prefix on the conda plugin in a tool dependencies conf file (yaml or xml)
galaxybot
@galaxybot
[enis] It definitely tries to install Conda and I was looking for conda_prefix but don’t see it in any of the config files. Can I just add it to server.ini?
John Chilton
@jmchilton
where ever the app properties are defined, if those are still in an ini file then yeah
galaxybot
@galaxybot
[enis] OK, that seems to have worked. Thanks!
John Chilton
@jmchilton
it finds these properties magically
Érica Souza
@souzaems
Captura de Tela 2018-10-15 às 15.22.28.png
Jennifer Hillman-Jackson
@jennaj
@souzaems Is this your Galaxy Biostars post? Even if not, it details how to get direct in contact with the usegalaxy.eu admins about the problem: https://biostar.usegalaxy.org/p/29701
They are doing some server maintainance and will be able to determine if there is really a Java issue or something else is going on with that particular server triggering the error
Érica Souza
@souzaems
Thank you very much =)
Martin Cech
@martenson
is there any application for bleach.clean(markupsafe.escape(user.value)) ?
Martin Cech
@martenson
asking for galaxyproject/galaxy#6871 (ping @nsoranzo )
@galaxybot the published items lost their 'header' in dev, is that intentional?
Nicola Soranzo
@nsoranzo
That's not part of the PR, not sure I understand the question.
Martin Cech
@martenson
@nsoranzo that is what the PR does right? it removes the markupsafe.escape but it still has the bleach.clean (wrapped in sanitize_html) which I think is fine
I am just curious whether that has some application
Nicola Soranzo
@nsoranzo
I think that escape() should have been the function left instead of sanitize_html(), I don't see reasons to allow any HTML tag there.
Martin Cech
@martenson
that is a good point, for some reason I treated them as equal
@guerler the published items lost their 'header' in dev, is that intentional?
Galaxy___Published_Workflow___Workflow_constructed_from_history__My_Project2_.png
Aysam Guerler
@guerler
Yes, it's on purpose, at least for now in dev. The options from the header are already available in the right panel afaik.